The problem of overweight and obesity in children and adolescents has been noted in many different countries. The aim of this study was to evaluate the differences in the percentage occurrence of overweight and obesity in Polish children depending on the criteria used, and to evaluate the usefulness of the Polish national database. The study sample comprised 3405 children aged 5–14 years (1674 girls and 1731 boys) from the city of Kraków, Poland, in 2009–2010. The BMI of each child was calculated and classified as overweight or obese according to three different reference BMI cut-offs: the International Obesity Task Force (IOTF), the Centers for Disease Control and Prevention (CDC) and the Polish 2010 standard. To assess the statistical significance of the differences between these three applied reference datasets, a comparison of two proportions was performed and Cohen’s kappa coefficient calculated. The prevalences of overweight were 15%, 11.3% and 9.5% (IOTF, CDC, Polish 2010, respectively) among boys and 15.5%, 11.6% and 9.9% among girls. The prevalences of obesity were 3.3%, 6.1% and 5.5% (IOTF, CDC, Polish 2010, respectively) among boys and 3.4%, 6.3% and 5.7% among girls. The different methods used generally showed good agreement. Nevertheless the prevalence of overweight and obesity differed significantly depending on the criteria used. In conclusion, the creation and updating of national databases based on large, representative groups is justified and provides the best reference for regional data. However, in order to ensure the comparability of results with those from other countries, it seems advisable to use cut-offs based on international data as well.